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Method: Accurate detection of tandem repeats from error-prone sequences with EquiRep
- Zhezheng Song,
- Tasfia Zahin,
- Xiang Li,
- and Mingfu Shao
Genome Res. December 2025 35: 2714-2721; Published in Advance August 21, 2025, doi:10.1101/gr.280750.125
...Zhezheng Song1,3, Tasfia Zahin1,3, Xiang Li1 and Mingfu Shao1,2 1Department of Computer Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA; 2Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802...
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Research: Hierarchical architecture of neo-sex chromosomes and accelerated adaptive evolution in tortricid moths
- Fangyuan Yang,
- Li-Jun Cao,
- Petr Nguyen,
- Zhong-Zheng Ma,
- Jin-Cui Chen,
- Wei Song,
- and Shu-Jun Wei
Genome Res. January 2025 35: 66-77; Published in Advance January 6, 2025, doi:10.1101/gr.279569.124
...Fangyuan Yang1,2, Li-Jun Cao1, Petr Nguyen3, Zhong-Zheng Ma1, Jin-Cui Chen1, Wei Song1 and Shu-Jun Wei1 1Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; 2Institute of Zoology, Chinese Academy of Science, Beijing 100101, China; 3Biology...
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Research: Dynamic A-to-I RNA editing in response to gut microbiome in honeybees
- Yuange Duan,
- Min Huang,
- Lin Ye,
- Ling Ma,
- Yashuai Wu,
- Yating Du,
- Jiyao Liu,
- Fan Song,
- Li Tian,
- Wanzhi Cai,
- Hu Li,
- Xin Zhou,
- and Shiqi Luo
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280291.124
...Yuange Duan,1 Min Huang,1 Lin Ye,1 Ling Ma, Yashuai Wu, Yating Du, Jiyao Liu, Fan Song, Li Tian, Wanzhi Cai, Hu Li, Xin Zhou, and Shiqi Luo State Key Laboratory of Agricultural and Forestry Biosecurity, MOA Key Laboratory of Pest Monitoring and Green Management, Department of Entomology, College...
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Method: Full-resolution HLA and KIR gene annotations for human genome assemblies
- Ying Zhou,
- Li Song,
- and Heng Li
Genome Res. November 2024 34: 1931-1941; Published in Advance June 5, 2024, doi:10.1101/gr.278985.124
...Full-resolution HLA and KIR gene annotations for human assemblies Ying Zhou1, Li Song2 and Heng Li1,3 1Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA; 2Department of Biomedical Data Science, Dartmouth College, Hanover, New Hampshire 03755, USA; 3...
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Method: QuadST identifies cell–cell interaction–changed genes in spatially resolved transcriptomics data
- Xiaoyu Song,
- Yuqing Shang,
- Michelle E. Ehrlich,
- Panos Roussos,
- Guo-Cheng Yuan,
- and Pei Wang
Genome Res. August 2025 35: 1821-1831; Published in Advance June 23, 2025, doi:10.1101/gr.279859.124
...QuadST identifies cell–cell interaction–changed genes in spatially resolved transcriptomics data Xiaoyu Song1, Yuqing Shang1, Michelle E. Ehrlich2, Panos Roussos3,4, Guo-Cheng Yuan5 and Pei Wang6 1Centre for Quantitative Medicine, Duke-NUS Medical School, Singapore 169857; 2Departments of Neurology...
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Method: Predicted protein 3D structures provide essential insights into the genetic architecture underlying phenotypic diversity in maize
- Shuai Wang,
- Merritt Khaipho-Burch,
- Lynn C. Johnson,
- Zachary R. Miller,
- Peter J. Bradbury,
- Doug Speed,
- William J. Allen,
- M. Cinta Romay,
- Jiquan Xue,
- Edward S. Buckler,
- Guillaume P. Ramstein,
- and Baoxing Song
Genome Res. January 2026 36: 214-225; Published in Advance October 31, 2025, doi:10.1101/gr.280514.125
...Shuai Wang1,2, Merritt Khaipho-Burch3, Lynn C. Johnson4, Zachary R. Miller4, Peter J. Bradbury5, Doug Speed6, William J. Allen7, M. Cinta Romay4, Jiquan Xue1, Edward S. Buckler3,4,5, Guillaume P. Ramstein6 and Baoxing Song1,2 1Key Laboratory of Maize Biology and Genetic Breeding in Arid Areas...
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Method: Homozygous editing of multiple genes for accelerated generation of xenotransplantation pigs
- Xiaoyue Duan,
- Chaolei Chen,
- Chang Du,
- Liang Guo,
- Jun Liu,
- Naipeng Hou,
- Pan Li,
- Xiaolan Qi,
- Fei Gao,
- Xuguang Du,
- Jiangping Song,
- and Sen Wu
Genome Res. May 2025 35: 1167-1178; Published in Advance March 5, 2025, doi:10.1101/gr.279709.124
...Xiaoyue Duan1,2,6, Chaolei Chen2,6, Chang Du2,6, Liang Guo1,2,6, Jun Liu2, Naipeng Hou1, Pan Li1,2, Xiaolan Qi3, Fei Gao1,2, Xuguang Du1,2, Jiangping Song1,4 and Sen Wu1,2,5 1Sanya Institute of China Agricultural University, Sanya, 572024, China; 2State Key Laboratory of Animal Biotech Breeding...
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Research: Chromatin interaction maps identify oncogenic targets of enhancer duplications in cancer
- Yueqiang Song,
- Fuyuan Li,
- Shangzi Wang,
- Yuntong Wang,
- Cong Lai,
- Lian Chen,
- Ning Jiang,
- Jin Li,
- Xingdong Chen,
- Swneke D. Bailey,
- and Xiaoyang Zhang
Genome Res. October 2024 34: 1514-1527; Published in Advance October 18, 2024, doi:10.1101/gr.278418.123
...Yueqiang Song1,6, Fuyuan Li1,6, Shangzi Wang1,6, Yuntong Wang1,7, Cong Lai1, Lian Chen1, Ning Jiang1, Jin Li1, Xingdong Chen1,2,3, Swneke D. Bailey4,5 and Xiaoyang Zhang1,8 1State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438...
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Research: Regeneration alters open chromatin and cis-regulatory landscape of erythroid precursors
- Yichao Zhou,
- Venkatasai Rahul Dogiparthi,
- Hannah L. Harris,
- Suhita Ray,
- Avik Choudhuri,
- Song Yang,
- Yi Zhou,
- Leonard I. Zon,
- M. Jordan Rowley,
- and Kyle J. Hewitt
Genome Res. July 2025 35: 1518-1529; Published in Advance June 2, 2025, doi:10.1101/gr.279949.124
...Yichao Zhou1, Venkatasai Rahul Dogiparthi1, Hannah L. Harris1, Suhita Ray1, Avik Choudhuri2, Song Yang2, Yi Zhou2, Leonard I. Zon2, M. Jordan Rowley1 and Kyle J. Hewitt1 1Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA; 2Howard...
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Method: Efficient and accurate KIR and HLA genotyping with massively parallel sequencing data
- Li Song,
- Gali Bai,
- X. Shirley Liu,
- Bo Li,
- and Heng Li
Genome Res. May 11, 2023 gr.277585.122; Published in Advance May 11, 2023, doi:10.1101/gr.277585.122
...Li Song1,2,4, Gali Bai1,5, X. Shirley Liu1,6, Bo Li3,7#, Heng Li1,2# 1: Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts 2: Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 3: Lyda Hill Department of Bioinformatics, University...
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